Variant report

Variant	rs2412682
Chromosome Location	chr15:42566987-42566988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr15:42565096-42567024	K562	blood:	n/a	n/a
2	MTA3	chr15:42564945-42567034	GM12878	blood:	n/a	n/a
3	MYC	chr15:42565122-42567080	K562	blood:	n/a	n/a
4	WRNIP1	chr15:42564953-42567418	GM12878	blood:	n/a	n/a
5	RCOR1	chr15:42565075-42567038	K562	blood:	n/a	n/a
6	POLR2A	chr15:42565058-42567059	GM12878	blood:	n/a	n/a
7	TBP	chr15:42565083-42566999	HepG2	liver:	n/a	n/a
8	HEY1	chr15:42565082-42566989	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:42564972-42567075	ProgFib	skin:	n/a	n/a
10	POLR2A	chr15:42565045-42567051	NB4	blood:	n/a	n/a
11	POLR2A	chr15:42565068-42567057	GM12892	blood:	n/a	n/a
12	MXI1	chr15:42564709-42567069	GM12878	blood:	n/a	n/a
13	GTF3C2	chr15:42565855-42567301	Hela-S3	cervix:	n/a	n/a
14	HCFC1	chr15:42564125-42567794	Hela-S3	cervix:	n/a	n/a
15	TBP	chr15:42564199-42567248	Hela-S3	cervix:	n/a	n/a
16	GTF3C2	chr15:42566783-42567604	K562	blood:	n/a	n/a
17	POLR2A	chr15:42564593-42567021	MCF10A-Er-Src	breast:	n/a	n/a
18	SMARCC1	chr15:42564666-42567115	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr15:42564823-42567120	PANC-1	pancreas:	n/a	n/a
20	MAX	chr15:42565143-42567875	NB4	blood:	n/a	chr15:42567154-42567161
21	UBTF	chr15:42565085-42567159	K562	blood:	n/a	n/a
22	POLR2A	chr15:42565132-42567054	GM19193	blood:	n/a	n/a
23	ARID3A	chr15:42566680-42567011	HepG2	liver:	n/a	n/a
24	RCOR1	chr15:42566837-42567121	HepG2	liver:	n/a	n/a
25	RPC155	chr15:42566765-42567302	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr15:42566934-42567039	K562	blood:	n/a	n/a
27	ZBTB7A	chr15:42566876-42567094	K562	blood:	n/a	n/a
28	MXI1	chr15:42564068-42568476	SK-N-SH	brain:	n/a	n/a
29	SMARCB1	chr15:42565144-42567045	Hela-S3	cervix:	n/a	n/a
30	RCOR1	chr15:42564607-42567069	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr15:42565014-42567783	HepG2	liver:	n/a	n/a
32	POLR2A	chr15:42565038-42567031	GM12891	blood:	n/a	n/a
33	MAFK	chr15:42564887-42567045	Hela-S3	cervix:	n/a	chr15:42566799-42566815 chr15:42566799-42566814 chr15:42566799-42566810 chr15:42566799-42566810
34	BHLHE40	chr15:42565191-42567220	K562	blood:	n/a	n/a
35	POLR2A	chr15:42564854-42567158	HL-60	blood:	n/a	n/a
36	GATA1	chr15:42564984-42567080	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42453296..42455922-chr15:42565346..42568176,2	K562	blood:
2	chr15:42565305..42567163-chr15:42839364..42842481,3	K562	blood:
3	chr15:42498938..42502268-chr15:42564432..42567193,3	MCF-7	breast:

Variant related genes	Relation type
GANC	TF binding region
TMEM87A	TF binding region
ENSG00000180979	Chromatin interaction
ENSG00000166887	Chromatin interaction
ENSG00000261002	Chromatin interaction
ENSG00000137814	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10775126	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851407	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851408	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851409	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631917	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631983	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638784	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438562	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12441642	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12441700	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594162	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12917101	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359003	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359004	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1619030	0.85[EUR][1000 genomes]
rs1659212	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659213	0.94[ASN][1000 genomes]
rs1659217	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659218	0.94[ASN][1000 genomes]
rs1659219	0.94[ASN][1000 genomes]
rs1659221	0.94[ASN][1000 genomes]
rs1659222	0.94[ASN][1000 genomes]
rs1678984	0.94[ASN][1000 genomes]
rs1678985	0.90[EUR][1000 genomes]
rs1678986	0.89[EUR][1000 genomes]
rs1678991	0.91[EUR][1000 genomes]
rs1678992	0.95[ASN][1000 genomes]
rs1678993	0.95[ASN][1000 genomes]
rs1679002	0.88[EUR][1000 genomes]
rs1679009	0.85[EUR][1000 genomes]
rs1679010	0.85[EUR][1000 genomes]
rs1703750	0.88[EUR][1000 genomes]
rs1703755	0.89[EUR][1000 genomes]
rs1712418	0.91[EUR][1000 genomes]
rs1712421	0.91[EUR][1000 genomes]
rs2138831	0.90[EUR][1000 genomes]
rs2289295	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407707	0.80[EUR][1000 genomes]
rs2412685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412705	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28364416	0.80[ASN][1000 genomes]
rs2918459	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918460	0.94[ASN][1000 genomes]
rs2918461	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743006	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850774	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4329897	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923940	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923943	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924645	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924653	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924660	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924674	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57002846	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57347762	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58313689	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59132828	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs598360	0.88[EUR][1000 genomes]
rs622442	0.85[EUR][1000 genomes]
rs633934	0.85[EUR][1000 genomes]
rs6493027	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493045	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs660126	0.89[EUR][1000 genomes]
rs677878	0.89[EUR][1000 genomes]
rs7086	0.80[EUR][1000 genomes]
rs71207359	0.82[AFR][1000 genomes]
rs7163495	0.82[AFR][1000 genomes]
rs7166785	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168709	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7169136	0.82[AFR][1000 genomes]
rs7175863	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7177120	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181742	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183015	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7183546	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73400993	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs751572	0.85[ASN][1000 genomes]
rs765830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024732	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025601	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8026198	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036046	0.94[EUR][1000 genomes]
rs8036187	0.94[EUR][1000 genomes]
rs8036380	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036596	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037020	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672382	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920921	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42563200-42567400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr15:42563400-42568200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:42563400-42568600	Active TSS	Right Atrium	heart
4	chr15:42563800-42567000	Active TSS	GM12878-XiMat	blood
5	chr15:42564000-42567000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr15:42564000-42567200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:42564000-42567600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr15:42564000-42568400	Active TSS	K562	blood
9	chr15:42564200-42567000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:42564200-42567000	Active TSS	A549	lung
11	chr15:42564400-42567000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:42564400-42567800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr15:42564400-42568400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr15:42564400-42568400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:42564600-42567000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:42564600-42567000	Active TSS	Left Ventricle	heart
17	chr15:42564600-42567600	Active TSS	Esophagus	oesophagus
18	chr15:42564600-42567600	Active TSS	Lung	lung
19	chr15:42564600-42567600	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr15:42564600-42567800	Bivalent/Poised TSS	HepG2	liver
21	chr15:42564600-42568000	Active TSS	Right Ventricle	heart
22	chr15:42564600-42568400	Active TSS	Aorta	Aorta
23	chr15:42564600-42568400	Active TSS	Ovary	ovary
24	chr15:42564800-42567000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr15:42564800-42567000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr15:42564800-42567000	Active TSS	Small Intestine	intestine
27	chr15:42564800-42568200	Active TSS	Colonic Mucosa	Colon
28	chr15:42565000-42567000	Active TSS	Duodenum Mucosa	Duodenum
29	chr15:42565000-42567000	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr15:42565000-42567200	Active TSS	Gastric	stomach
31	chr15:42565200-42567000	Active TSS	Spleen	Spleen
32	chr15:42565800-42567200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr15:42565800-42567200	Flanking Active TSS	NH-A	brain
34	chr15:42565800-42567800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr15:42565800-42568400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr15:42565800-42568400	Flanking Active TSS	HUVEC	blood vessel
37	chr15:42565800-42568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:42565800-42568600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr15:42565800-42568600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr15:42566000-42567200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr15:42566000-42567400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr15:42566000-42567800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr15:42566000-42567800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:42566000-42567800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr15:42566000-42568400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:42566000-42568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:42566000-42568600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr15:42566000-42568800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:42566200-42567400	Flanking Active TSS	Fetal Brain Female	brain
50	chr15:42566400-42567000	Flanking Active TSS	Fetal Thymus	thymus

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